2016 Morning Poster Presentation Abstracts
Scroll down below to view abstracts listed in order of session and department. Click on the links below, organized by topic area to skip to a specific session.
Morning Sessions by Topic - 9:00 - 10:50 AM
Biochemistry, Cellular & Molecular Biology
Vanessa Nguyen
Graduate Student, Biochemistry, Cellular & Molecular Biology
Title: A Novel Soluble Peptide with pH-Responsive Membrane Insertion
Abstract: Cancer is characterized by acidification of the extracellular environment. Acidosis can be employed as a target to specifically direct therapies to the diseased tissue. We have used first principles to design an acidity-triggered rational membrane (ATRAM) peptide with high solubility in solution that is able to interact with lipid membranes in a pH dependent fashion. Biophysical studies show that the ATRAM peptide binds to the surface of lipid membranes at pH 8.0. However, acidification leads to the peptide inserting into the lipid bilayer as a transmembrane α-helix. The insertion of ATRAM into membranes occurs at a moderately acidic pH (with a pK of 6.5), similar to the extracellular pH found in solid tumors. Studies with human cell lines showed a highly efficient pH-dependent membrane targeting, without causing toxicity. We show that it is possible to rationally design a soluble peptide that selectively targets cell membranes in acidic environments.
Abstract: Cancer is characterized by acidification of the extracellular environment. Acidosis can be employed as a target to specifically direct therapies to the diseased tissue. We have used first principles to design an acidity-triggered rational membrane (ATRAM) peptide with high solubility in solution that is able to interact with lipid membranes in a pH dependent fashion. Biophysical studies show that the ATRAM peptide binds to the surface of lipid membranes at pH 8.0. However, acidification leads to the peptide inserting into the lipid bilayer as a transmembrane α-helix. The insertion of ATRAM into membranes occurs at a moderately acidic pH (with a pK of 6.5), similar to the extracellular pH found in solid tumors. Studies with human cell lines showed a highly efficient pH-dependent membrane targeting, without causing toxicity. We show that it is possible to rationally design a soluble peptide that selectively targets cell membranes in acidic environments.
Lindsey O'Neal
Graduate Student, Biochemistry, Cellular & Molecular Biology
Title: C-di-GMP Mediates Aerotaxis and Receptor Sensitivity
Abstract: Azospirillum brasilense are motile proteobacteria capable of movement in oxygen gradients (aerotaxis). Aerotaxis is the strongest behavioral response in this species which can be observed by the formation of a sharp arerotactic band at some distance from the meniscus when cells are exposed to a spatial gradient of oxygen. Aerotaxis, including aerotactic band formation, is mediated by several chemotaxis receptors including Tlp1. Tlp1 is a prototypical transmembrane chemotaxis receptor which also possesses a c-di-GMP effector domain (PilZ) at the extreme C-terminus. We have previously shown that c-di-GMP binding to the PilZ domain of Tlp1 affected the sensitivity of the receptor and impaired aerotaxis. However, the physiological significance for c-di-GMP regulating a chemotaxis receptor’s sensitivity is not known. Here, we developed an optogenetic tool for the real-time manipulation of intracellular c-di-GMP metabolism in swimming bacteria, and we used it to characterize the role of c-di-GMP signaling during aerotaxis in A. brasilense. First, we showed that this optogenetic system allows manipulation of c-di-GMP metabolism at time scales relevant to chemotaxis since it mediates immediate, yet transient increases or decreases in c-di-GMP content, since the effects dissipate within 10 minutes. Second, we demonstrated that c-di-GMP itself is not a cue sensed by aerotaxis receptors since increasing c-di-GMP or decreasing c-di-GMP content of free-swimming cells did not affect their motility patterns. Using a mutant altered in c-di-GMP metabolism and additional aerotaxis assays, we also provide evidence that c-di-GMP likely regulates the sensitivity of most, if not all, receptors that contribute to the formation of a sharp aerotactic band in A. brasilense, suggesting a function for three other PilZ-containing receptors. Last we provide evidence that c-di-GMP binding to receptors has a direct role in mediating response time to changes in aeration.
Abstract: Azospirillum brasilense are motile proteobacteria capable of movement in oxygen gradients (aerotaxis). Aerotaxis is the strongest behavioral response in this species which can be observed by the formation of a sharp arerotactic band at some distance from the meniscus when cells are exposed to a spatial gradient of oxygen. Aerotaxis, including aerotactic band formation, is mediated by several chemotaxis receptors including Tlp1. Tlp1 is a prototypical transmembrane chemotaxis receptor which also possesses a c-di-GMP effector domain (PilZ) at the extreme C-terminus. We have previously shown that c-di-GMP binding to the PilZ domain of Tlp1 affected the sensitivity of the receptor and impaired aerotaxis. However, the physiological significance for c-di-GMP regulating a chemotaxis receptor’s sensitivity is not known. Here, we developed an optogenetic tool for the real-time manipulation of intracellular c-di-GMP metabolism in swimming bacteria, and we used it to characterize the role of c-di-GMP signaling during aerotaxis in A. brasilense. First, we showed that this optogenetic system allows manipulation of c-di-GMP metabolism at time scales relevant to chemotaxis since it mediates immediate, yet transient increases or decreases in c-di-GMP content, since the effects dissipate within 10 minutes. Second, we demonstrated that c-di-GMP itself is not a cue sensed by aerotaxis receptors since increasing c-di-GMP or decreasing c-di-GMP content of free-swimming cells did not affect their motility patterns. Using a mutant altered in c-di-GMP metabolism and additional aerotaxis assays, we also provide evidence that c-di-GMP likely regulates the sensitivity of most, if not all, receptors that contribute to the formation of a sharp aerotactic band in A. brasilense, suggesting a function for three other PilZ-containing receptors. Last we provide evidence that c-di-GMP binding to receptors has a direct role in mediating response time to changes in aeration.
Yue Ma
Graduate Student, Biochemistry, Cellular & Molecular Biology
Title: Non-detergent Isolation of Cyanobacterial Photosystem I Using SMALPs (Styrene Maleic Acid Lipid Particles) 2.QM/MM and Molecular Dynamic Simulations of transfer in Ubiquitin-like NEDD8 RING E3-E2 ̴UBL-target Complex
Abstract: For over thirty years, photosynthetic reaction centers have been isolated using non-ionic detergents. However, as membrane proteins, these reaction centers are surrounded and interact with lipids, which are easily removed during traditional purification methods by small molecular detergent. Treatment with these surfactants results in mixed micelles that contain both the detergent and some of the native lipids from the membrane. To date only a small number of the native, bound lipids have been resolved using X-ray crystallography. In present work, we report a novel, non-detergent method of isolating cyanobacterial PSI using a styrene maleic anhydride (SMA) copolymer. SMA copolymers are characterized by the presence of alternating charged and hydrophobic groups. 2. Ubiquitin-like (UBL) protein modification of substrate proteins plays a key role in regulating protein function. Unlike ubiquitin (UB) and small ubiquitin-like modifier (SUMO) which are ligated to a massive segment of the proteome, the UBL NEDD8 is highly selective on modifying closely related cullin proteins (CULs) on a single lysine residue and contributes to 10% - 20% of all cellular ubiquitination. In this study, the X-structure of a trapped E3-E2 ̴ NEDD8-target intermediate (RBX1-UBC12 ̴ NEDD8-CUL1-DCN1) is used to build computer models and combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations are performed to investigate the catalytic mechanism of the NEDD8 transfer from E2 to the substrate with the nucleophillic addition of activated Lys720 of the substrate to Gly76. The role of the active site residues is examined, and it is demonstrated that Lys720 not only performs the nucleophilic attack during the catalysis, but also acts as a general acid catalyst to protonate the leaving group of C111 of UBC12.
Abstract: For over thirty years, photosynthetic reaction centers have been isolated using non-ionic detergents. However, as membrane proteins, these reaction centers are surrounded and interact with lipids, which are easily removed during traditional purification methods by small molecular detergent. Treatment with these surfactants results in mixed micelles that contain both the detergent and some of the native lipids from the membrane. To date only a small number of the native, bound lipids have been resolved using X-ray crystallography. In present work, we report a novel, non-detergent method of isolating cyanobacterial PSI using a styrene maleic anhydride (SMA) copolymer. SMA copolymers are characterized by the presence of alternating charged and hydrophobic groups. 2. Ubiquitin-like (UBL) protein modification of substrate proteins plays a key role in regulating protein function. Unlike ubiquitin (UB) and small ubiquitin-like modifier (SUMO) which are ligated to a massive segment of the proteome, the UBL NEDD8 is highly selective on modifying closely related cullin proteins (CULs) on a single lysine residue and contributes to 10% - 20% of all cellular ubiquitination. In this study, the X-structure of a trapped E3-E2 ̴ NEDD8-target intermediate (RBX1-UBC12 ̴ NEDD8-CUL1-DCN1) is used to build computer models and combined quantum mechanics/molecular mechanics (QM/MM) and molecular dynamics (MD) simulations are performed to investigate the catalytic mechanism of the NEDD8 transfer from E2 to the substrate with the nucleophillic addition of activated Lys720 of the substrate to Gly76. The role of the active site residues is examined, and it is demonstrated that Lys720 not only performs the nucleophilic attack during the catalysis, but also acts as a general acid catalyst to protonate the leaving group of C111 of UBC12.
Seda Kocaman
Graduate Student, Biochemistry, Cellular & Molecular Biology
Title: The role of solvent effect on the aminoglycoside-binding properties of thermophilic and mesophilic variants of Aminoglycoside Nucleotidyltransferase 4' (ANT4)
Abstract: Aminoglycosides are a group of antibiotics that bind to the 16s ribosome RNA of prokaryotes and thereby cause mistranslations and premature stops which interfere with protein translation. Some bacterial species developed resistance against aminoglycosides due to their aminoglycoside modifying enzymes (AGMEs). Aminoglycoside nucleotidyltransferase 4' (ANT4) is an AGME which transfers the AMP group from MgATP to the C4’-OH of aminoglycosides in order to detoxify them. Two thermostable variants (T130K and D80Y) of ANT4 have been created in our laboratory by introducing single point mutations to the wild type (WT) ANT4. Our group has shown earlier that; local flexibility and ligand binding properties of T130K resembles the mesophilic WT enzyme whereas D80Y, which has the highest melting temperature, presents distinct features representative of a true thermophilic enzyme. This work is based on the hypothesis that solvent reorganization upon ligand binding may be used to identify properties that lead to thermophilicity. Since the active sites of ANT4' are highly solvent exposed, binding of ligands will cause (or be affected by) differential solvent reorganization. Therefore, we are investigating the solvent reorganization on the aminoglycoside-binding properties of different ANT4 variants via performing isothermal titration calorimetry (ITC) both in light water (H2O ) and heavy water (D2O ).
Abstract: Aminoglycosides are a group of antibiotics that bind to the 16s ribosome RNA of prokaryotes and thereby cause mistranslations and premature stops which interfere with protein translation. Some bacterial species developed resistance against aminoglycosides due to their aminoglycoside modifying enzymes (AGMEs). Aminoglycoside nucleotidyltransferase 4' (ANT4) is an AGME which transfers the AMP group from MgATP to the C4’-OH of aminoglycosides in order to detoxify them. Two thermostable variants (T130K and D80Y) of ANT4 have been created in our laboratory by introducing single point mutations to the wild type (WT) ANT4. Our group has shown earlier that; local flexibility and ligand binding properties of T130K resembles the mesophilic WT enzyme whereas D80Y, which has the highest melting temperature, presents distinct features representative of a true thermophilic enzyme. This work is based on the hypothesis that solvent reorganization upon ligand binding may be used to identify properties that lead to thermophilicity. Since the active sites of ANT4' are highly solvent exposed, binding of ligands will cause (or be affected by) differential solvent reorganization. Therefore, we are investigating the solvent reorganization on the aminoglycoside-binding properties of different ANT4 variants via performing isothermal titration calorimetry (ITC) both in light water (H2O ) and heavy water (D2O ).
Ramya Enganti
Graduate Student, Biochemistry, Cellular & Molecular Biology
Title: Characterizing the role of RPS6 phosphorylation in Arabidopsis thaliana
Abstract: Translational regulation in eukaryotic cells is a key process required to maintain protein levels under various environmental conditions to regulate growth and development. One such protein subjected to translational control is ribosomal protein of small subunit 6 (RPS6), which as the name suggests, is part of the eukaryotic 40S subunit. It is highly conserved among all eukaryotes and has been shown to undergo phosphorylation at multiple sites in its C-terminal tail. The phosphorylation is regulated in response to various environmental stresses such as mitogens, cold, heat shock and hypoxia and also light conditions (in plants). While this has been observed in several eukaryotes, its functional significance is still unclear. Recent studies in mammals have provided evidence for RPS6 phosphorylation in playing a role in regulating cell size, translation and ribosome biogenesis, however, very little is known about its role in plants. Arabidopsis RPS6 is encoded by two genes, RPS6A and RPS6B, and the two proteins are functionally equivalent. Double knockout leads to embryo lethality, however, single rps6 mutants are viable but show developmental defects including pointed leaves, short primary roots and reduced pollen viability. We hypothesize that RPS6 phosphorylation plays a role in regulating cell growth and translation in Arabidopsis. To understand the role of this phosphorylation, we have designed several phospho-null (serine to alanine mutations) and phospho-mimic (serine to aspartate) constructs with various combinations of the mutated residues. We have also generated transgenic lines with the various versions of the mutated RPS6 in the mutant background. These transgenic lines are currently being used to carry out phenotypic analyses under various stress conditions.
Abstract: Translational regulation in eukaryotic cells is a key process required to maintain protein levels under various environmental conditions to regulate growth and development. One such protein subjected to translational control is ribosomal protein of small subunit 6 (RPS6), which as the name suggests, is part of the eukaryotic 40S subunit. It is highly conserved among all eukaryotes and has been shown to undergo phosphorylation at multiple sites in its C-terminal tail. The phosphorylation is regulated in response to various environmental stresses such as mitogens, cold, heat shock and hypoxia and also light conditions (in plants). While this has been observed in several eukaryotes, its functional significance is still unclear. Recent studies in mammals have provided evidence for RPS6 phosphorylation in playing a role in regulating cell size, translation and ribosome biogenesis, however, very little is known about its role in plants. Arabidopsis RPS6 is encoded by two genes, RPS6A and RPS6B, and the two proteins are functionally equivalent. Double knockout leads to embryo lethality, however, single rps6 mutants are viable but show developmental defects including pointed leaves, short primary roots and reduced pollen viability. We hypothesize that RPS6 phosphorylation plays a role in regulating cell growth and translation in Arabidopsis. To understand the role of this phosphorylation, we have designed several phospho-null (serine to alanine mutations) and phospho-mimic (serine to aspartate) constructs with various combinations of the mutated residues. We have also generated transgenic lines with the various versions of the mutated RPS6 in the mutant background. These transgenic lines are currently being used to carry out phenotypic analyses under various stress conditions.
Daiane Santana Alves
Postdoc, Biochemistry, Cellular & Molecular Biology
Title: Roxy‐7: a novel peptide that activates the EphA2 receptor
Abstract: The erythropoietin-producing hepatocellular carcinoma (Eph) receptor is involved in several key processes such as cell proliferation, migration, differentiation and apoptosis, which help to maintain cell cycle homeostasis. Dysregulation of these cellular processes perturbs the tight physiological control of healthy cells and can give rise to the pathological states implicated in the development of cancer. A key receptor for these processes in humans, EphA2, is overexpressed in several cancers with poor outcomes. The differential expression of EphA2 in some cancer types compared to normal cells highlights its importance as a therapeutic target. Despite its overexpression, multiple studies have documented low levels of EphA2 phosphorylation in malignant cells. In the present work, we designed a peptide (Roxy-7) that targets the EphA2 receptor and significantly increases EphA2 phosphorylation (p-Tyr) in non-small cell lung cancer (NSCLC) in vitro. Roxy-7 is soluble until acidity triggers its insertion into lipid bilayers and adoption of α-helical secondary structure, highlighting a potential targeting mechanism. Structured Illumination Microscopy (SIM) experiments indicate that Roxy-7 enhances endogenous EphA2 receptor clustering at the plasma membrane. We also tested the toxicity of the peptide in cancer cells by MTS assay and the results show that Roxy-7 is not toxic. Finally and most importantly, Roxy-7 inhibits cell migration in two different cancer cell line models suggesting that Roxy-7 has potential for metastasis treatment. In summary, here we investigate a new potential therapeutic molecule that enhances phosphorylation of EphA2 receptor and inhibits cell migration.
Abstract: The erythropoietin-producing hepatocellular carcinoma (Eph) receptor is involved in several key processes such as cell proliferation, migration, differentiation and apoptosis, which help to maintain cell cycle homeostasis. Dysregulation of these cellular processes perturbs the tight physiological control of healthy cells and can give rise to the pathological states implicated in the development of cancer. A key receptor for these processes in humans, EphA2, is overexpressed in several cancers with poor outcomes. The differential expression of EphA2 in some cancer types compared to normal cells highlights its importance as a therapeutic target. Despite its overexpression, multiple studies have documented low levels of EphA2 phosphorylation in malignant cells. In the present work, we designed a peptide (Roxy-7) that targets the EphA2 receptor and significantly increases EphA2 phosphorylation (p-Tyr) in non-small cell lung cancer (NSCLC) in vitro. Roxy-7 is soluble until acidity triggers its insertion into lipid bilayers and adoption of α-helical secondary structure, highlighting a potential targeting mechanism. Structured Illumination Microscopy (SIM) experiments indicate that Roxy-7 enhances endogenous EphA2 receptor clustering at the plasma membrane. We also tested the toxicity of the peptide in cancer cells by MTS assay and the results show that Roxy-7 is not toxic. Finally and most importantly, Roxy-7 inhibits cell migration in two different cancer cell line models suggesting that Roxy-7 has potential for metastasis treatment. In summary, here we investigate a new potential therapeutic molecule that enhances phosphorylation of EphA2 receptor and inhibits cell migration.
Sarah Alouani
Undergraduate Student, Biochemistry, Cellular & Molecular Biology
Title: Exploring Granuloma Formation in Johne’s Disease
Abstract: Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne’s disease in domestic animals and wildlife. By examining its pathological changes, it was found that MAP infection naturally induces formation of granuloma (persistent structures containing bacteria, macrophages, and lymphocytes), that are thought to restrict the spread of MAP infection. The process of granuloma formation has not been clearly defined. This study aims to better understand the mechanism of granuloma formation through in vitro and in silico studies. Using the results of in vitro experiments, we will analyze dynamics and functions of granulomas using a computer program, NetLogo. This study will reveal many aspects of macrophage behaviour, such as movement, interaction, death rate, bactericidal effects, etc. This study may lead to the discovery of a Johne’s disease treatment which acts through modification of granuloma induction.
Abstract: Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne’s disease in domestic animals and wildlife. By examining its pathological changes, it was found that MAP infection naturally induces formation of granuloma (persistent structures containing bacteria, macrophages, and lymphocytes), that are thought to restrict the spread of MAP infection. The process of granuloma formation has not been clearly defined. This study aims to better understand the mechanism of granuloma formation through in vitro and in silico studies. Using the results of in vitro experiments, we will analyze dynamics and functions of granulomas using a computer program, NetLogo. This study will reveal many aspects of macrophage behaviour, such as movement, interaction, death rate, bactericidal effects, etc. This study may lead to the discovery of a Johne’s disease treatment which acts through modification of granuloma induction.
Kristen Booth
Undergraduate Student, Biochemistry Cellular & Molecular Biology
Title: Roxy7: A potential new pH-dependent peptide with implications for tumor targeting
Abstract: Development, both normal and oncogenic, is regulated, in part, by Eph receptor tyrosine kinases and their associated ligands, called ephrins. One member of this family is EphA2. EphA2 has been cited in numerous studies for its overexpression in multiple cancers that present with poor prognoses. Non-cancerous cells express low levels of EphA2, which when it stably binds to its ligand ephrinA1, reduces the amount of extracellular matrix attachments, decreases cell migration, and inhibits malignant growth. Cancer cells that overexpress EphA2 do not participate in this stable ligand-binding, and instead can acquire ligand-independent pro-oncogenic functions through the activation of the Akt and RSK pathways. Moreover, this signaling pathway leads to the phosphorylation of the tyrosine kinase domain of EphA2, prompting receptor clustering and endocytosis. Our laboratory designed a peptide called Roxy7 in hopes that through a pH-dependent manner it could specifically target cancer cells in the acidic tumor microenvironment (TME). Upon recognition, Roxy7 would insert into the cell membrane and interact with EphA2, increasing the phosphorylation of the tyrosine kinase domain needed to inhibit the Akt and RSK signaling pathways and ultimately decrease the migration and invasiveness of cancer cells. Here, I wanted to see if Roxy7 is able to bind to the cell membrane and, if so, how well does it bind. In order to achieve this goal, we are using an NBD binding assay at multiple pH values and comparing the fluorescence intensity to the negative control peptide Roxy8. Our results indicated that the fluorescence intensity partition coefficient (Kp) of Roxy7 at pH 8 is 7.99x105 ± 7.2x105, at pH 7 is 3.91x105 ± 9.11x104, at pH 6 in 4.42x105 ± 4.89x104, and at pH 5 is 1.39x106 ± 2.07x105. This shows an increase in binding as the environment acidifies, which suggests that Roxy7 is capable of inserting into a cancer cell’s membrane in a pH-dependent manner.
Abstract: Development, both normal and oncogenic, is regulated, in part, by Eph receptor tyrosine kinases and their associated ligands, called ephrins. One member of this family is EphA2. EphA2 has been cited in numerous studies for its overexpression in multiple cancers that present with poor prognoses. Non-cancerous cells express low levels of EphA2, which when it stably binds to its ligand ephrinA1, reduces the amount of extracellular matrix attachments, decreases cell migration, and inhibits malignant growth. Cancer cells that overexpress EphA2 do not participate in this stable ligand-binding, and instead can acquire ligand-independent pro-oncogenic functions through the activation of the Akt and RSK pathways. Moreover, this signaling pathway leads to the phosphorylation of the tyrosine kinase domain of EphA2, prompting receptor clustering and endocytosis. Our laboratory designed a peptide called Roxy7 in hopes that through a pH-dependent manner it could specifically target cancer cells in the acidic tumor microenvironment (TME). Upon recognition, Roxy7 would insert into the cell membrane and interact with EphA2, increasing the phosphorylation of the tyrosine kinase domain needed to inhibit the Akt and RSK signaling pathways and ultimately decrease the migration and invasiveness of cancer cells. Here, I wanted to see if Roxy7 is able to bind to the cell membrane and, if so, how well does it bind. In order to achieve this goal, we are using an NBD binding assay at multiple pH values and comparing the fluorescence intensity to the negative control peptide Roxy8. Our results indicated that the fluorescence intensity partition coefficient (Kp) of Roxy7 at pH 8 is 7.99x105 ± 7.2x105, at pH 7 is 3.91x105 ± 9.11x104, at pH 6 in 4.42x105 ± 4.89x104, and at pH 5 is 1.39x106 ± 2.07x105. This shows an increase in binding as the environment acidifies, which suggests that Roxy7 is capable of inserting into a cancer cell’s membrane in a pH-dependent manner.
Alison Krenzer
Undergraduate Student, Biochemistry, Cellular & Molecular Biology
Title: The Effect of Hormones and ISE2 on Intercellular Trafficking in Nicotiana benthamiana
Abstract: A requirement for intercellular communication in plants is microscopic cytoplasmic channels, plasmodesmata, which facilitate trafficking of micro- and macromolecules between cells. The purpose of this study was to compare the effects on intercellular trafficking of various plant hormones in Nicotiana benthamiana. The hormones used were salicylic acid (SA), abscisic acid (ABA), and auxin (IAA). SA is involved in plant immunity, regulates cell-to-cell permeability during immune response, and induces plasmodesmata callose deposition and closure. ABA plays an important role in the plant responses to environmental stress and pathogens. IAA is essential for cell growth because it affects both cell division and cellular expansion. These hormones were applied onto wild-type plants, and transgenic plants that constitutively express high levels of plasmodesmata-regulating protein INCREASED SIZE EXCULSION LIMIT2 (ISE2). OE1 and OE3 are two of these transgenic lines. Mutant ise2 embryos contain more twinned or branched plasmodesmata than do sibling wild-type embryos. This results in an increase of plasmodesmata mediated movement. ISE2 is a chloroplast-localized protein and its altered expression may lead to hormone imbalances in the transgenic plants. We present data on the levels of the various hormones in the wild-type, OE1, and OE3 lines, and we also show how exogenous application of SA, ABA, and IAA effect plasmodesmata-mediated intercellular trafficking.
Abstract: A requirement for intercellular communication in plants is microscopic cytoplasmic channels, plasmodesmata, which facilitate trafficking of micro- and macromolecules between cells. The purpose of this study was to compare the effects on intercellular trafficking of various plant hormones in Nicotiana benthamiana. The hormones used were salicylic acid (SA), abscisic acid (ABA), and auxin (IAA). SA is involved in plant immunity, regulates cell-to-cell permeability during immune response, and induces plasmodesmata callose deposition and closure. ABA plays an important role in the plant responses to environmental stress and pathogens. IAA is essential for cell growth because it affects both cell division and cellular expansion. These hormones were applied onto wild-type plants, and transgenic plants that constitutively express high levels of plasmodesmata-regulating protein INCREASED SIZE EXCULSION LIMIT2 (ISE2). OE1 and OE3 are two of these transgenic lines. Mutant ise2 embryos contain more twinned or branched plasmodesmata than do sibling wild-type embryos. This results in an increase of plasmodesmata mediated movement. ISE2 is a chloroplast-localized protein and its altered expression may lead to hormone imbalances in the transgenic plants. We present data on the levels of the various hormones in the wild-type, OE1, and OE3 lines, and we also show how exogenous application of SA, ABA, and IAA effect plasmodesmata-mediated intercellular trafficking.
Akshita Patel
Undergraduate Student, Biochemistry, Cellular & Molecular Biology
Title: Characterization of Nicotiana benthamiana Plants Overexpressing ISE2
Abstract: INCREASED SIZE EXCLUSION LIMIT2 (ISE2) is a chloroplast protein. Chloroplasts have many synthetic capabilities including carbon fixation, protein and starch synthesis, as well as the production of hormones that regulate plant growth and development. It has been shown that decreased levels of ISE2 expression disrupts chloroplast development. In this study, we examined how increased ISE2 expression can affect chloroplast function. We hypothesized that changes in ISE2 overexpression would change the function of chloroplast, especially starch accumulation and chlorophyll production. In this project, starch accumulation and chlorophyll production in transgenic Nicotiana benthamiana plants overexpressing ISE2 were characterized. The results were compared between wild type plants and different overexpressing ISE2 plants. The analysis of the results supports the idea that overexpression of ISE2 genes changes starch and chlorophyll production in N. benthamiana plants.
Abstract: INCREASED SIZE EXCLUSION LIMIT2 (ISE2) is a chloroplast protein. Chloroplasts have many synthetic capabilities including carbon fixation, protein and starch synthesis, as well as the production of hormones that regulate plant growth and development. It has been shown that decreased levels of ISE2 expression disrupts chloroplast development. In this study, we examined how increased ISE2 expression can affect chloroplast function. We hypothesized that changes in ISE2 overexpression would change the function of chloroplast, especially starch accumulation and chlorophyll production. In this project, starch accumulation and chlorophyll production in transgenic Nicotiana benthamiana plants overexpressing ISE2 were characterized. The results were compared between wild type plants and different overexpressing ISE2 plants. The analysis of the results supports the idea that overexpression of ISE2 genes changes starch and chlorophyll production in N. benthamiana plants.
Chemical & Biomolecular Engineering
Nelly Cantillo
Graduate Student, Chemical & Biomolecular Engineering
Title: Microstructure Characterization of a PEMFC Catalyst Layer: Effect on Performance
Abstract: Proton Exchange Membrane Fuel Cells (PEMFC) are considered one of the most promising alternative energy technologies due to the low operation temperature, compact structure and wide range of applications, among other advantages. The demand for low platinum loading in PEMFC electrodes has driven recent research on electrode structure-function correlations. The structure and morphology of the electrode layer play important roles in controlling many aspects of fuel cell performance. Within the catalyst layers (CLs), the hydrogen oxidation and the oxygen reduction reactions take place, involving complex mass and charge transport processes (diffusion of reactants and products, migration and diffusion of protons, migration of electrons, permeation, electroosmotic drag, as well as vaporization/condensation of water). In this study, the microstructure of PEMFC electrodes with different variations in terms of ionomer to carbon (IC) ratios, ionomer equivalent weights and electrode thickness (by means of variations in Pt loading) were evaluated by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Brunauer-Emmett-Teller (BET) nitrogen adsorption, including materials dispersion and porosity in CLs for freestanding electrodes. Several typical features can be determined by TEM characterization, providing indications of the large-scale porosity of the layer as well as images showing expanses of ionomer with and without embedded Pt particles. In previous studies, measurements of water transport in similar CLs suggested that sub-saturated catalyst layers have a less connected ionomer network than that expected from uniform coverage of particles in the layer. Microscopy and other measurements noted above on a series of systematically modified catalyst layers will be summarized in an attempt to assess this finding. Single cell performance with these catalyst layers was evaluated in order to analyze the relationship with the structure properties.
Abstract: Proton Exchange Membrane Fuel Cells (PEMFC) are considered one of the most promising alternative energy technologies due to the low operation temperature, compact structure and wide range of applications, among other advantages. The demand for low platinum loading in PEMFC electrodes has driven recent research on electrode structure-function correlations. The structure and morphology of the electrode layer play important roles in controlling many aspects of fuel cell performance. Within the catalyst layers (CLs), the hydrogen oxidation and the oxygen reduction reactions take place, involving complex mass and charge transport processes (diffusion of reactants and products, migration and diffusion of protons, migration of electrons, permeation, electroosmotic drag, as well as vaporization/condensation of water). In this study, the microstructure of PEMFC electrodes with different variations in terms of ionomer to carbon (IC) ratios, ionomer equivalent weights and electrode thickness (by means of variations in Pt loading) were evaluated by scanning electron microscopy (SEM), transmission electron microscopy (TEM) and Brunauer-Emmett-Teller (BET) nitrogen adsorption, including materials dispersion and porosity in CLs for freestanding electrodes. Several typical features can be determined by TEM characterization, providing indications of the large-scale porosity of the layer as well as images showing expanses of ionomer with and without embedded Pt particles. In previous studies, measurements of water transport in similar CLs suggested that sub-saturated catalyst layers have a less connected ionomer network than that expected from uniform coverage of particles in the layer. Microscopy and other measurements noted above on a series of systematically modified catalyst layers will be summarized in an attempt to assess this finding. Single cell performance with these catalyst layers was evaluated in order to analyze the relationship with the structure properties.
Madeline Hayes
Unergraduate Student, Chemical & Biomolecular Engineering
Title: Arachnoid Cyst Surgical Treatment: A Meta Analysis of the Current Literature
Abstract: Arachnoid cysts typically form during embryonic development by the splitting of the arachnoid membrane which then fills with cerebrospinal fluid (CSF) forming a cyst, and are therefore classified as congenital anomalies. However, these cysts can also form due to a traumatic head impact. Arachnoid cysts are generally benign and can be asymptomatic or symptomatic. In cases where patient symptoms are indicated, the effects of arachnoid cysts can be disabling. These symptoms include incapacitating pain, loss of motor function, severe dizziness, vision impairment, and psychiatric effects. Currently, there is very little quantitative evidence addressing whether or not surgery is an effective treatment to relieve symptoms, and doctors are more likely to recommend the conservative approach of pain management. The primary objective of this research was to perform a meta analysis of available data to evaluate the effectiveness of the three most common surgical treatments (craniotomy, endoscopic fenestration, and shunting) in relieving patient symptoms. The technical approach to accomplish this objective included an overarching literature review performed in the PubMed database, which references reliable articles of medicine from around the world, and a subsequent meta analysis of the collected data. A global study was performed based on all of the viable data to investigate the overall surgical effectiveness including patients of all ages. Given a previous study on pediatrics alone, a more detailed study was performed on adults of age 18 and older. The results of this study indicate that surgery is an effective option to reduce or eliminate symptoms. A comprehensive summary of the meta analysis along with an overview of arachnoid cysts and available treatment methods will be provided on the proposed poster. In particular, correlations noted across patient data and their possible effects on the rate of surgical success will be presented.
Abstract: Arachnoid cysts typically form during embryonic development by the splitting of the arachnoid membrane which then fills with cerebrospinal fluid (CSF) forming a cyst, and are therefore classified as congenital anomalies. However, these cysts can also form due to a traumatic head impact. Arachnoid cysts are generally benign and can be asymptomatic or symptomatic. In cases where patient symptoms are indicated, the effects of arachnoid cysts can be disabling. These symptoms include incapacitating pain, loss of motor function, severe dizziness, vision impairment, and psychiatric effects. Currently, there is very little quantitative evidence addressing whether or not surgery is an effective treatment to relieve symptoms, and doctors are more likely to recommend the conservative approach of pain management. The primary objective of this research was to perform a meta analysis of available data to evaluate the effectiveness of the three most common surgical treatments (craniotomy, endoscopic fenestration, and shunting) in relieving patient symptoms. The technical approach to accomplish this objective included an overarching literature review performed in the PubMed database, which references reliable articles of medicine from around the world, and a subsequent meta analysis of the collected data. A global study was performed based on all of the viable data to investigate the overall surgical effectiveness including patients of all ages. Given a previous study on pediatrics alone, a more detailed study was performed on adults of age 18 and older. The results of this study indicate that surgery is an effective option to reduce or eliminate symptoms. A comprehensive summary of the meta analysis along with an overview of arachnoid cysts and available treatment methods will be provided on the proposed poster. In particular, correlations noted across patient data and their possible effects on the rate of surgical success will be presented.
Samira Ibrahim
Undergraduate Student, Chemical & Biomolecular Engineering
Title: Robust and Cost Efficient Method for Fabrication of Tungsten Tips for Scanning Tunneling Microscopy
Abstract: The quest for green energy has sparked considerable interest in Photosystem I (PS I), the photosynthetic protein complex, that acts like a nano-scale biological photodiode and enables light-activated charge separation (with nearly~100% quantum efficiency) to facilitate unidirectional electron flow. The structural and photo-electrochemical properties of PS I make it suitable for incorporation into bio-electronic or hybrid photochemical devices. But, the first step towards the rational design of such devices requires a fundamental understanding of the morphological and electronic properties of PS I on various donor substrates/electrodes. Scanning Tunneling Microscopy (STM) is a powerful scanning-probe technique that allows simultaneous high-resolution analysis of localized topography and charge transport properties of at atomistic resolution. To this end, preparation of quality STM tips is critical in acquiring high quality images and in turn tunneling current of PS I nanostructures. Such demand for high-precision STM tips has launched the exploration of many techniques used to produce STM tips with uniform and controlled tip radius and geometry. Each of these methods is marked by distinct parameters which demand highly specific configurations. Our method, facilitated by electrochemical (EC) etching of tungsten wire, allows the creation of sharp and clean STM tips via judicious selection of the process parameters. In this presentation an overview of our novel device that produces robust, efficient tips that provide the design and operation of our affordable, cutting-edge alternative to costly manufacturing of STM tips will be discussed.
Abstract: The quest for green energy has sparked considerable interest in Photosystem I (PS I), the photosynthetic protein complex, that acts like a nano-scale biological photodiode and enables light-activated charge separation (with nearly~100% quantum efficiency) to facilitate unidirectional electron flow. The structural and photo-electrochemical properties of PS I make it suitable for incorporation into bio-electronic or hybrid photochemical devices. But, the first step towards the rational design of such devices requires a fundamental understanding of the morphological and electronic properties of PS I on various donor substrates/electrodes. Scanning Tunneling Microscopy (STM) is a powerful scanning-probe technique that allows simultaneous high-resolution analysis of localized topography and charge transport properties of at atomistic resolution. To this end, preparation of quality STM tips is critical in acquiring high quality images and in turn tunneling current of PS I nanostructures. Such demand for high-precision STM tips has launched the exploration of many techniques used to produce STM tips with uniform and controlled tip radius and geometry. Each of these methods is marked by distinct parameters which demand highly specific configurations. Our method, facilitated by electrochemical (EC) etching of tungsten wire, allows the creation of sharp and clean STM tips via judicious selection of the process parameters. In this presentation an overview of our novel device that produces robust, efficient tips that provide the design and operation of our affordable, cutting-edge alternative to costly manufacturing of STM tips will be discussed.
Michelle Lehmann
Undergraduate Student, Chemical & Biomolecular Engineering
Title: Recovery of Phenolic Compounds from a Non-Structural Fraction of Switchgrass
Abstract: The separation and recovery of soluble phenolic compounds from switchgrass potentially provides an additional income stream to facilities producing biofuel from switchgrass. Phenolic compounds from plants can be used in the pharmaceutical, cosmetic and nutritional industries. They are also known to have antioxidant and anti-inflammatory properties. Switchgrass is desirable as a feed stock for biofuel as it can be grown on underutilized land where there is little or no competition with land currently used for food production. The objectives of this study were to obtain information using a surrogate compound so that the feasibility of the process can be estimated and demonstrate the proof of principal for recovering phenolic compounds from switchgrass extracts. The selected surrogate phenol compound is gallic acid (GA). A process based on the sorption of extracted phenolics from water onto activated carbon followed by desorption into alcohol appears to be feasible. Results indicate that the use of GA as a surrogate for extracted phenolics of switchgrass extract is useful, though less likely to desorb than the phenolics. The improved ability to recover sorbed switchgrass phenolics is a positive indication. More studies are however necessary to establish a complete and usable process. Other sorption media are also an attractive alternative technology.
Abstract: The separation and recovery of soluble phenolic compounds from switchgrass potentially provides an additional income stream to facilities producing biofuel from switchgrass. Phenolic compounds from plants can be used in the pharmaceutical, cosmetic and nutritional industries. They are also known to have antioxidant and anti-inflammatory properties. Switchgrass is desirable as a feed stock for biofuel as it can be grown on underutilized land where there is little or no competition with land currently used for food production. The objectives of this study were to obtain information using a surrogate compound so that the feasibility of the process can be estimated and demonstrate the proof of principal for recovering phenolic compounds from switchgrass extracts. The selected surrogate phenol compound is gallic acid (GA). A process based on the sorption of extracted phenolics from water onto activated carbon followed by desorption into alcohol appears to be feasible. Results indicate that the use of GA as a surrogate for extracted phenolics of switchgrass extract is useful, though less likely to desorb than the phenolics. The improved ability to recover sorbed switchgrass phenolics is a positive indication. More studies are however necessary to establish a complete and usable process. Other sorption media are also an attractive alternative technology.
Alexandra Galaska
Undergraduate Student, Chemical & Biomolecular Engineering
Title: Effects of Epoxy 385 When Combined with Magnesium Hydroxide and Melamine Polyphosphate for Industrial Purposes
Abstract: This presentation reviews the test results of the combination of two flame retardants: melamine polyphosphate and magnesium hydroxide, with epoxy resin 385. Epoxy is a polyepoxide, a class of reactive prepolymers and polymers which contain epoxide groups. Used in a wide range of applications that, when formed, creates a thermosetting polymer, often with high mechanical properties, temperature and chemical resistance; certain properties to be more suitable for the desired product. Magnesium hydroxide is an inorganic flame retardant and melamine polyphosphate is an effective phosphorus-based flame retardant commonly used in the industry. The effects and comparison of pure epoxy, versus a single flame retardant versus both flame retardants combined, all at specific weight percentage has been specified.
Abstract: This presentation reviews the test results of the combination of two flame retardants: melamine polyphosphate and magnesium hydroxide, with epoxy resin 385. Epoxy is a polyepoxide, a class of reactive prepolymers and polymers which contain epoxide groups. Used in a wide range of applications that, when formed, creates a thermosetting polymer, often with high mechanical properties, temperature and chemical resistance; certain properties to be more suitable for the desired product. Magnesium hydroxide is an inorganic flame retardant and melamine polyphosphate is an effective phosphorus-based flame retardant commonly used in the industry. The effects and comparison of pure epoxy, versus a single flame retardant versus both flame retardants combined, all at specific weight percentage has been specified.
Kaitlin Oliver Butler
Graduate Student, Biochemistry, Cellular & Molecular Biology
Title: A Linkage-Based Mechanism with Variable Curvature
Abstract: We propose a novel, tendon-driven mechanism for minimally invasive surgery that can conform to a curved path and withstand externally applied forces without deflection as well as deliver high-magnitude forces at the end effector. The design consists of a concatenated series of rigid-link, crossed, four-bar mechanisms that are synchronized to produce uniform, variable curvature motion in one degree of freedom. As a tool for minimally invasive surgery, it offers potential for improved performance for tough- or hard-tissue procedures, e.g. in orthopedic surgeries. A prototype that is an appropriate scale for minimally invasive surgery was 3D printed and tested for load bearing capability, where the mechanism's rigidity was confirmed. Future work will focus on obtaining multiple degrees of freedom and constructing both a large- and small-scale metal prototype for improved strength.
Abstract: We propose a novel, tendon-driven mechanism for minimally invasive surgery that can conform to a curved path and withstand externally applied forces without deflection as well as deliver high-magnitude forces at the end effector. The design consists of a concatenated series of rigid-link, crossed, four-bar mechanisms that are synchronized to produce uniform, variable curvature motion in one degree of freedom. As a tool for minimally invasive surgery, it offers potential for improved performance for tough- or hard-tissue procedures, e.g. in orthopedic surgeries. A prototype that is an appropriate scale for minimally invasive surgery was 3D printed and tested for load bearing capability, where the mechanism's rigidity was confirmed. Future work will focus on obtaining multiple degrees of freedom and constructing both a large- and small-scale metal prototype for improved strength.
Microbiology
Julianna Burchett
Undergraduate Student, Microbiology
Title: Metabolic response of autobioluminescent yeast and human cells in the presence of cellulose nanocrystals (CNCs)
Abstract: Cellulose nanocrystals (CNCs) are widely used in different industries including pharmaceutical and cosmetic production due to their adept physical and biological properties. Because CNCs are becoming a more prevalent material and have a high potential of being redistributed in the environment, it is important to understand their toxic potentials in biological systems, including organisms of various trophic levels. This study evaluated the cytotoxic effects of CNCs in the lower eukaryotic organism Saccharomyces cerevisiae and human embryonic kidney (HEK293) cells using autobioluminescent yeast and human cell reporters, respectively. The S. cerevisiae and HEK293 reporter cells were engineered to express a synthetic bacterial luciferase operon (luxCDABE) that self-generates all the required substrates for bioluminescent production. As a result, these reporter cells allow for continuousmonitoring of the same cell population throughout the period of toxicant exposure, providing a facile means for tracking the temporal dynamics of toxic effects on living cells. When exposed to CNCs at concentrations ranging from 0.001 g/L to 1 g/L, both the yeast and human cells reported time and dose-dependent effects. Exposure to CNCs at 0.001 g/L and 1 g/L reduced bioluminescent output in S. cerevisiae by 5% and 10% compared to untreated control cells 8 hours post-treatment, respectively, and further decreased the signal by 25% and 70% 12 hours post-treatment, respectively. In HEK293 cells, treatment with CNCs at 1 g/L initialized a significant decrease (by 23%) in metabolic activity at 2 days post-treatment, and the bioluminescent output continued to decline to less than 10% compared to untreated controls at 7 days post-treatment. CNCs at 0.001 g/L did not result in significant changes in metabolic activity throughout the entire period of exposure. These results demonstrate the cytotoxic potential for elevated concentrations of CNCs in varying biological systems.
Abstract: Cellulose nanocrystals (CNCs) are widely used in different industries including pharmaceutical and cosmetic production due to their adept physical and biological properties. Because CNCs are becoming a more prevalent material and have a high potential of being redistributed in the environment, it is important to understand their toxic potentials in biological systems, including organisms of various trophic levels. This study evaluated the cytotoxic effects of CNCs in the lower eukaryotic organism Saccharomyces cerevisiae and human embryonic kidney (HEK293) cells using autobioluminescent yeast and human cell reporters, respectively. The S. cerevisiae and HEK293 reporter cells were engineered to express a synthetic bacterial luciferase operon (luxCDABE) that self-generates all the required substrates for bioluminescent production. As a result, these reporter cells allow for continuousmonitoring of the same cell population throughout the period of toxicant exposure, providing a facile means for tracking the temporal dynamics of toxic effects on living cells. When exposed to CNCs at concentrations ranging from 0.001 g/L to 1 g/L, both the yeast and human cells reported time and dose-dependent effects. Exposure to CNCs at 0.001 g/L and 1 g/L reduced bioluminescent output in S. cerevisiae by 5% and 10% compared to untreated control cells 8 hours post-treatment, respectively, and further decreased the signal by 25% and 70% 12 hours post-treatment, respectively. In HEK293 cells, treatment with CNCs at 1 g/L initialized a significant decrease (by 23%) in metabolic activity at 2 days post-treatment, and the bioluminescent output continued to decline to less than 10% compared to untreated controls at 7 days post-treatment. CNCs at 0.001 g/L did not result in significant changes in metabolic activity throughout the entire period of exposure. These results demonstrate the cytotoxic potential for elevated concentrations of CNCs in varying biological systems.
Biosystems Engineering & Soil Science
Marie English
Graduate Student, Biosystems Engineering & Soil Science
Title: Effects of Biodegradable Plastic Mulch Treatments on Soil Carbon Dynamics
Abstract: Plastic agricultural mulches are commonly used to grow crops because they provide moisture retention, temperature optimization and decreased soil erosion. Currently, the most common feedstock used to produce these mulches is fossil fuel-based polyethylene plastic. Unlike polyethylene plastic mulches, biodegradable plastic mulches (BDMs) consist of polymers that are recognizable as food by naturally occurring soil microorganisms. As a result, BDMs can be biodegraded into carbon dioxide, water, and microbial biomass as part of the soil carbon cycle. As the BDMs break down, there is a direct addition of carbon into the soil which can affect soil organic matter formation. This addition of carbon and increased soil moisture and temperature can also have potential feedbacks on soil quality by impacting microbial activity and nutrient cycles. This study compares four commercially available biodegradable mulches, polyethylene mulch, cellulose mulch and bare ground to see the impacts on the soil carbon cycle. Field trials are being conducted at Northwestern Washington Research and Extension Center, Mount Vernon, WA, and at East Tennessee Research and Education Center, Knoxville, TN. A USDA soil quality assessment before the growing season and after harvest serve to provide data on whether the mulch treatments are altering soil nutrient cycles. Measurements of respiration, total organic carbon, microbial biomass, extracellular enzyme activity and density fractionation will provide insight on the partitioning of carbon between the passive and active pools of carbon. After the first growing season, there were no significant differences in respiration rates between mulch treatments but significant differences were observed between the Tennessee and Washington sites. Throughout this study, we will continue to monitor the different pools and fluxes of carbon to better understand what mechanisms are most important in the carbon dynamics of mulch covered soils.
Abstract: Plastic agricultural mulches are commonly used to grow crops because they provide moisture retention, temperature optimization and decreased soil erosion. Currently, the most common feedstock used to produce these mulches is fossil fuel-based polyethylene plastic. Unlike polyethylene plastic mulches, biodegradable plastic mulches (BDMs) consist of polymers that are recognizable as food by naturally occurring soil microorganisms. As a result, BDMs can be biodegraded into carbon dioxide, water, and microbial biomass as part of the soil carbon cycle. As the BDMs break down, there is a direct addition of carbon into the soil which can affect soil organic matter formation. This addition of carbon and increased soil moisture and temperature can also have potential feedbacks on soil quality by impacting microbial activity and nutrient cycles. This study compares four commercially available biodegradable mulches, polyethylene mulch, cellulose mulch and bare ground to see the impacts on the soil carbon cycle. Field trials are being conducted at Northwestern Washington Research and Extension Center, Mount Vernon, WA, and at East Tennessee Research and Education Center, Knoxville, TN. A USDA soil quality assessment before the growing season and after harvest serve to provide data on whether the mulch treatments are altering soil nutrient cycles. Measurements of respiration, total organic carbon, microbial biomass, extracellular enzyme activity and density fractionation will provide insight on the partitioning of carbon between the passive and active pools of carbon. After the first growing season, there were no significant differences in respiration rates between mulch treatments but significant differences were observed between the Tennessee and Washington sites. Throughout this study, we will continue to monitor the different pools and fluxes of carbon to better understand what mechanisms are most important in the carbon dynamics of mulch covered soils.
Materials Science & Engineering
Valerie Garcia-Negron
Graduate Student, Materials Science & Engineering
Title: Sustainable Energy Systems: High Performance Lithium Ion Battery Components from Renewable Resources
Abstract: Lignin is an abundant organic polymer found mostly in vascular plants that has potential applications due to its complex cross-linked interactions. Hardwood and softwood lignin exists in nature with several structure variants making it a versatile compound in the production of pulp, biomass, biofuels and carbon materials. The heterogeneous nature of lignin feedstocks makes elucidation of the relationship between processing and the resulting material structure difficult to predict. Investigation of the processing and the structure relationships in lignin-based materials can provide an understanding, which leads to optimized materials with targeted properties. In this work, we examined the role of unit operations in the carbonization process of lignin. Specifically, we varied the presence, temperature and duration of thermal stabilization, pyrolysis and passivation. We also examined the effect of ball milling techniques. The resulting materials were characterized at the atomic and micro-scales using x-ray diffraction, elemental analysis, and electron microscopy. High temperature carbonization produced a greater graphitization, which has been shown to correlate with charge capacities. Consequently, a properly designed carbonization process for lignin is well suited to generating low-cost, high-efficiency electrodes for next generation Lithium ion batteries. Characterization of the electrochemical behavior of coin cell batteries using lignin-based electrodes shows competitive performance compared to traditional graphite electrodes, at a fraction of the cost.
Abstract: Lignin is an abundant organic polymer found mostly in vascular plants that has potential applications due to its complex cross-linked interactions. Hardwood and softwood lignin exists in nature with several structure variants making it a versatile compound in the production of pulp, biomass, biofuels and carbon materials. The heterogeneous nature of lignin feedstocks makes elucidation of the relationship between processing and the resulting material structure difficult to predict. Investigation of the processing and the structure relationships in lignin-based materials can provide an understanding, which leads to optimized materials with targeted properties. In this work, we examined the role of unit operations in the carbonization process of lignin. Specifically, we varied the presence, temperature and duration of thermal stabilization, pyrolysis and passivation. We also examined the effect of ball milling techniques. The resulting materials were characterized at the atomic and micro-scales using x-ray diffraction, elemental analysis, and electron microscopy. High temperature carbonization produced a greater graphitization, which has been shown to correlate with charge capacities. Consequently, a properly designed carbonization process for lignin is well suited to generating low-cost, high-efficiency electrodes for next generation Lithium ion batteries. Characterization of the electrochemical behavior of coin cell batteries using lignin-based electrodes shows competitive performance compared to traditional graphite electrodes, at a fraction of the cost.
Mahshid Ahmadi
Postdoc, Materials Science & Engineering
Title: Photo-generated Dipole Effect on Photovoltaic Performance in Organo-metal Halide Perovskite Solar Cells
Abstract: Solar is the most abundant renewable energy source. In recent years, solar energy has been seen as one of the most promising renewable energy sources. Therefore the research into solar cells and the development of the technology has gain more importance. The relatively high cost of solar energy conversion compared to that of fossil sources is still a major hurdle preventing the widespread adoption of PV technologies. Therefore, cost reduction is crucial. The recent development in some novel materials has opened up new possibilities for the production of low-cost and highly efficient solar cells. Research offers strong power out puts from low cost materials that are relatively simple to produce into working devices. Organo-metallic halide perovskite solar cells are one of the hottest prospects in low cost solar energy technology. The first perovskite cells were made in 2009 and the best confirmed can already convert 20.1% of the energy in sunlight into electricity. That’s starting to be competitive with commercial thin-film cells like cadmium telluride and silicon. However, it has proven difficult to make high quality perovskite solar cells consistently. Here, fabrication and characterization of highly efficient perovskite solar cells is reported. Judicious choice of transport layer in perovskite solar cells can be one of the essential parameters in solar cells design and fabrication techniques. Certain fundamental issues need to be addressed in order to further enhance the performance of perovskite solar cells, for instance, designing new transport layers to minimize recombination loss at the perovskite layer. Factors other than mobility and energy level alignment must be taken into accounts in the hole transport layer to further improve the performance of perovskite solar cells. Here the results indicate the role of dipoles on the charge dissociation and charge recombination in perovskite solar cells. The higher efficiency is rationalized to the influence of partially aligned photo-generated dipoles in transport layer which reduces the charge recombination and enhances the charge dissociation and transport in perovskite solar cells.
Abstract: Solar is the most abundant renewable energy source. In recent years, solar energy has been seen as one of the most promising renewable energy sources. Therefore the research into solar cells and the development of the technology has gain more importance. The relatively high cost of solar energy conversion compared to that of fossil sources is still a major hurdle preventing the widespread adoption of PV technologies. Therefore, cost reduction is crucial. The recent development in some novel materials has opened up new possibilities for the production of low-cost and highly efficient solar cells. Research offers strong power out puts from low cost materials that are relatively simple to produce into working devices. Organo-metallic halide perovskite solar cells are one of the hottest prospects in low cost solar energy technology. The first perovskite cells were made in 2009 and the best confirmed can already convert 20.1% of the energy in sunlight into electricity. That’s starting to be competitive with commercial thin-film cells like cadmium telluride and silicon. However, it has proven difficult to make high quality perovskite solar cells consistently. Here, fabrication and characterization of highly efficient perovskite solar cells is reported. Judicious choice of transport layer in perovskite solar cells can be one of the essential parameters in solar cells design and fabrication techniques. Certain fundamental issues need to be addressed in order to further enhance the performance of perovskite solar cells, for instance, designing new transport layers to minimize recombination loss at the perovskite layer. Factors other than mobility and energy level alignment must be taken into accounts in the hole transport layer to further improve the performance of perovskite solar cells. Here the results indicate the role of dipoles on the charge dissociation and charge recombination in perovskite solar cells. The higher efficiency is rationalized to the influence of partially aligned photo-generated dipoles in transport layer which reduces the charge recombination and enhances the charge dissociation and transport in perovskite solar cells.
Cody Pratt
Undergraduate Student, Materials Science & Engineering
Title: Point Defect Analysis in MoSe2 Derived by Mechanical Exfoliation and Chemical Vapor Deposition
Abstract: Two-dimensional MoSe2 is a semiconductor with a direct bandgap making it a promising material for nanoelectronic and optoelectronic applications. This investigation studies the point defects in MoSe2 derived from two different synthesis methods. One technique used to isolate these monolayer films is referred to as mechanical exfoliation or otherwise known as the scotch tape method. In a recent paper by Huang et al, an improved method of mechanical exfoliation is outlined. Where they focus on isolating graphene from bulk graphite, we extend this to a transition metal dichalcogenide and show that this new mechanical exfoliation process more reliably produces single layer flakes. The second synthesis method looked at is chemical vapor deposition method where single layers are grown from a gaseous precursor at high temperatures, rather than isolating from a bulk crystal. Characterization of sample is done with electron energy-loss spectroscopy (EELS) which gives information of chemical composition and bonding; as well as, optical properties and Z-contrast microscopy performed on the state-of-the-art fifth-order-aberration correction Nion UltraSTEM which produces atomic resolution images for direct point defect observation. We investigate, through electron energy-loss spectroscopy and high-spatial resolution Z-contrast imaging, whether the number of point defects in chemical vapor deposition grown materials is greater than the point defect concentration of mechanically exfoliated two dimensional materials. The defect concentration plays a vital role to charge carrier concentration because each point defect acts as a scattering site to charge carriers. Finally, we suggest ways to decrease the amount of point defects in MoSe2 from chemical vapor deposition since chemical vapor deposition method is the most applicable for large scale production of these materials when they find themselves integrated into current technology.
Abstract: Two-dimensional MoSe2 is a semiconductor with a direct bandgap making it a promising material for nanoelectronic and optoelectronic applications. This investigation studies the point defects in MoSe2 derived from two different synthesis methods. One technique used to isolate these monolayer films is referred to as mechanical exfoliation or otherwise known as the scotch tape method. In a recent paper by Huang et al, an improved method of mechanical exfoliation is outlined. Where they focus on isolating graphene from bulk graphite, we extend this to a transition metal dichalcogenide and show that this new mechanical exfoliation process more reliably produces single layer flakes. The second synthesis method looked at is chemical vapor deposition method where single layers are grown from a gaseous precursor at high temperatures, rather than isolating from a bulk crystal. Characterization of sample is done with electron energy-loss spectroscopy (EELS) which gives information of chemical composition and bonding; as well as, optical properties and Z-contrast microscopy performed on the state-of-the-art fifth-order-aberration correction Nion UltraSTEM which produces atomic resolution images for direct point defect observation. We investigate, through electron energy-loss spectroscopy and high-spatial resolution Z-contrast imaging, whether the number of point defects in chemical vapor deposition grown materials is greater than the point defect concentration of mechanically exfoliated two dimensional materials. The defect concentration plays a vital role to charge carrier concentration because each point defect acts as a scattering site to charge carriers. Finally, we suggest ways to decrease the amount of point defects in MoSe2 from chemical vapor deposition since chemical vapor deposition method is the most applicable for large scale production of these materials when they find themselves integrated into current technology.
Chemistry
Laura Casto
Graduate Student, Chemistry
Title: Development of an Immunoassay for β-endorphin Using Capillary Electrophoresis
Abstract: Capillary electrophoresis immunoassays (CE-IAs) offer many advantages over other immunoassay formats, including small sample volumes, reduced costs, quick analysis time, and automation capabilities. These advantages are particularly desirable for advancing towards real-time analysis of neuropeptide hormone secretion profiles from on-line cell cultures. The dysregulation of β-endorphin, an endogenous opioid peptide found in the hypothalamus and pituitary gland, may be involved in the pathology of Autism Spectrum Disorders (ASD). β-endorphin is known to exert regulatory effects on the secretion of oxytocin, which is a key hormone in the development and maintenance of social bonding behavior. To understand potential roles of β-endorphin dysregulation in ASD, we must first be able to measure β-endorphin secretion with high temporal resolution in basal models. This work aims to develop the first CE-IA for β-endorphin. Here we discuss the optimization of CE conditions to achieve analytical separation of β-endorphin and a β-endorphin-specific IgG antibody. The challenge of protein adsorption to capillary walls is discussed, and buffer additive methods for overcoming this challenge are presented. Special consideration is given to buffer additives that do not obscure UV absorbance detection. Future directions for adapting the current assay to LED-induced fluorescence detection are proposed.
Abstract: Capillary electrophoresis immunoassays (CE-IAs) offer many advantages over other immunoassay formats, including small sample volumes, reduced costs, quick analysis time, and automation capabilities. These advantages are particularly desirable for advancing towards real-time analysis of neuropeptide hormone secretion profiles from on-line cell cultures. The dysregulation of β-endorphin, an endogenous opioid peptide found in the hypothalamus and pituitary gland, may be involved in the pathology of Autism Spectrum Disorders (ASD). β-endorphin is known to exert regulatory effects on the secretion of oxytocin, which is a key hormone in the development and maintenance of social bonding behavior. To understand potential roles of β-endorphin dysregulation in ASD, we must first be able to measure β-endorphin secretion with high temporal resolution in basal models. This work aims to develop the first CE-IA for β-endorphin. Here we discuss the optimization of CE conditions to achieve analytical separation of β-endorphin and a β-endorphin-specific IgG antibody. The challenge of protein adsorption to capillary walls is discussed, and buffer additive methods for overcoming this challenge are presented. Special consideration is given to buffer additives that do not obscure UV absorbance detection. Future directions for adapting the current assay to LED-induced fluorescence detection are proposed.
Brianna Watson
Graduate Student, Chemistry
Title: Nonlinear Imaging of Transition Dipole Moment Orientation and Morphology in Hybrid Organic-Inorganic Perovskite Films
Abstract: Hybrid organic-inorganic perovskites have shown great potential as new solar materials; however, in order to eventually surpass silicon as the industry standard, it is necessary to understand how the processing of these materials affects their interactions with light. In previous studies, it has been shown that thermal annealing affects the quality of the perovskite film in regards to both the size of crystalline domains and conversion efficiency. By utilizing polarization-resolved two-photon total internal reflectance fluorescence microscopy (TIRFM), we were able to image the transformation of the dipole moment orientation in hybrid organic-inorganic lead-iodide-based perovskite (CH3NH3PbI3) thin films on glass during the thermal annealing process and changes in the topology of the film. It was shown in our studies that the distribution of transition dipole moments with in-plane orientation increased over two hours of thermal annealing. Two-photon TIRFM, due to its axial sensitivity, also provides insight into the topography, as seen in the signal intensity of the collected fluorescence images. From these measurements it was concluded that the films become more axially homogeneous during the thermal annealing process. These results provide new considerations when designing preparation and processing techniques aimed at increasing the efficiency of perovskite as a photovoltaic material.
Abstract: Hybrid organic-inorganic perovskites have shown great potential as new solar materials; however, in order to eventually surpass silicon as the industry standard, it is necessary to understand how the processing of these materials affects their interactions with light. In previous studies, it has been shown that thermal annealing affects the quality of the perovskite film in regards to both the size of crystalline domains and conversion efficiency. By utilizing polarization-resolved two-photon total internal reflectance fluorescence microscopy (TIRFM), we were able to image the transformation of the dipole moment orientation in hybrid organic-inorganic lead-iodide-based perovskite (CH3NH3PbI3) thin films on glass during the thermal annealing process and changes in the topology of the film. It was shown in our studies that the distribution of transition dipole moments with in-plane orientation increased over two hours of thermal annealing. Two-photon TIRFM, due to its axial sensitivity, also provides insight into the topography, as seen in the signal intensity of the collected fluorescence images. From these measurements it was concluded that the films become more axially homogeneous during the thermal annealing process. These results provide new considerations when designing preparation and processing techniques aimed at increasing the efficiency of perovskite as a photovoltaic material.
Amber Moody
Graduate Student, Chemistry
Title: SESORS for Neuroscience
Abstract: Current cerebral imaging techniques lack the ability to measure local concentrations of neurochemicals in the brain. Gaining this ability would aid in understanding brain function and the development of neurological diseases. The local concentrations of neurochemicals have only been probed using invasive techniques that involve drilling holes in the skull. Using the combination of two powerful Raman spectroscopies, surface enhanced Raman spectroscopy (SERS) and spatially offset Raman spectroscopy (SORS), a non-invasive method for measurements of neurochemicals through the skull is presented. SERS provides a greatly enhanced Raman signal from low concentrations of analytes that have been adsorbed to noble metal nanoparticles giving the capability to identify and quantify biomolecules. SORS allows for Raman signal to be obtained from subsurface layers of turbid media by collecting the spectra at a set distance away from the illumination point. Here we demonstrate surface enhanced SORS, termed SESORS, for measurements of SERS active nanoparticles coated with various neurochemicals through skull bone. This approach allows for skin-safe laser illumination levels while maintaining the ability to probe low concentrations of neurochemicals.
Abstract: Current cerebral imaging techniques lack the ability to measure local concentrations of neurochemicals in the brain. Gaining this ability would aid in understanding brain function and the development of neurological diseases. The local concentrations of neurochemicals have only been probed using invasive techniques that involve drilling holes in the skull. Using the combination of two powerful Raman spectroscopies, surface enhanced Raman spectroscopy (SERS) and spatially offset Raman spectroscopy (SORS), a non-invasive method for measurements of neurochemicals through the skull is presented. SERS provides a greatly enhanced Raman signal from low concentrations of analytes that have been adsorbed to noble metal nanoparticles giving the capability to identify and quantify biomolecules. SORS allows for Raman signal to be obtained from subsurface layers of turbid media by collecting the spectra at a set distance away from the illumination point. Here we demonstrate surface enhanced SORS, termed SESORS, for measurements of SERS active nanoparticles coated with various neurochemicals through skull bone. This approach allows for skin-safe laser illumination levels while maintaining the ability to probe low concentrations of neurochemicals.
Sahar Rostom
Graduate Student, Chemistry
Title: Determination of Tracer Diffusion Coefficients of Soft Nanoparticles in a Polymer Matrix using Neutron Reflectivity
Abstract: The addition of nanoparticles to a polymer matrix can fine tune its properties and lead to a novel material with interesting behavior. These nanoparticles may also alter the dynamics of the polymer chain by slowing down or increasing diffusion, which will impact the processability and properties of the new composite material. In a previous study, we have shown that the diffusion of 535 K dPS in PS is increased by the addition of soft PS nanoparticles of different sizes and shapes. In this study, we extend our work by developing a novel method to determine the tracer diffusion coefficient of these nanoparticles. Neutron reflectivity is used to monitor the mutual diffusion between a bilayer that consists of pure 535k and a nanoparticle. At very long annealing times, the system exhibits diffusive behavior, where the classical Fickian analysis can be applied. Moreover, we extract the tracer diffusion coefficients of the nanoparticles by applying the slow mode theory. Our results show that the nanoparticles are fairly mobile and cannot be considered stationary, as is often assumed in the examination of the dynamics of polymer chains in polymer nanocomposites
Abstract: The addition of nanoparticles to a polymer matrix can fine tune its properties and lead to a novel material with interesting behavior. These nanoparticles may also alter the dynamics of the polymer chain by slowing down or increasing diffusion, which will impact the processability and properties of the new composite material. In a previous study, we have shown that the diffusion of 535 K dPS in PS is increased by the addition of soft PS nanoparticles of different sizes and shapes. In this study, we extend our work by developing a novel method to determine the tracer diffusion coefficient of these nanoparticles. Neutron reflectivity is used to monitor the mutual diffusion between a bilayer that consists of pure 535k and a nanoparticle. At very long annealing times, the system exhibits diffusive behavior, where the classical Fickian analysis can be applied. Moreover, we extract the tracer diffusion coefficients of the nanoparticles by applying the slow mode theory. Our results show that the nanoparticles are fairly mobile and cannot be considered stationary, as is often assumed in the examination of the dynamics of polymer chains in polymer nanocomposites
Sara Isbill
Graduate Student, Chemistry
Title: Theoretical Studies of Catalysis by Silver and Vanadium Surfaces
Abstract: While transition metals are commonly used to catalyze the oxidation of small organic compounds, the mechanisms of these reactions are not well understood. Two oxidation reactions on metal surfaces that have been deeply studied at the fundamental level using both experiment and theory are ethylene epoxidation on the silver (111) surface and methanol formation on the vanadium (100) surface. While significant strides have been taken towards revealing the complex chemical pathways of these surface reactions, several aspects of the catalysis, particularly the different ways in which oxygen interacts with the catalyst as well as with the reactants have yet to be elucidated. This understanding is critical for designing better catalysts for these important reactions. Preliminary results of density functional theory (DFT) calculations of the adsorption of atomic oxygen on the Ag(111) surface show that oxygen prefers to bind to the hollow sites rather than the bridge site, and weakly binds to the on-top site. Our results also show that oxygen prefers to occupy on octahedral subsurface site but can easily diffuse to the surface when placed in an inverted tetrahedron subsurface site, indicating this site may be important for oxygen movement between the surface and subsurface. Preliminary results of DFT calculations of the adsorption of atomic oxygen on the V(100) surface show that oxygen prefers to bind to the hollow site but binds strongly to all high-symmetry sites. Methane has been shown to physisorb to the clean vanadium surface, yielding H and CH3 after dissociation which favor hollow and bridge sites, respectively. While much work remains to be done on these systems, the current results are in good agreement with available experimental results.
Abstract: While transition metals are commonly used to catalyze the oxidation of small organic compounds, the mechanisms of these reactions are not well understood. Two oxidation reactions on metal surfaces that have been deeply studied at the fundamental level using both experiment and theory are ethylene epoxidation on the silver (111) surface and methanol formation on the vanadium (100) surface. While significant strides have been taken towards revealing the complex chemical pathways of these surface reactions, several aspects of the catalysis, particularly the different ways in which oxygen interacts with the catalyst as well as with the reactants have yet to be elucidated. This understanding is critical for designing better catalysts for these important reactions. Preliminary results of density functional theory (DFT) calculations of the adsorption of atomic oxygen on the Ag(111) surface show that oxygen prefers to bind to the hollow sites rather than the bridge site, and weakly binds to the on-top site. Our results also show that oxygen prefers to occupy on octahedral subsurface site but can easily diffuse to the surface when placed in an inverted tetrahedron subsurface site, indicating this site may be important for oxygen movement between the surface and subsurface. Preliminary results of DFT calculations of the adsorption of atomic oxygen on the V(100) surface show that oxygen prefers to bind to the hollow site but binds strongly to all high-symmetry sites. Methane has been shown to physisorb to the clean vanadium surface, yielding H and CH3 after dissociation which favor hollow and bridge sites, respectively. While much work remains to be done on these systems, the current results are in good agreement with available experimental results.
Andrea Becker
Graduate Student, Chemistry
Title: A computational investigation of molecular junctions using electronic structure theory
Abstract: Molecular junctions are the smallest form of nanoelectronic circuits, consisting of one molecule bound between two electrodes. The properties of these junctions have been of great interest to the scientific community for decades; however, there is still much unknown about the transport of electrons through the junction, and how it is affected by various physical and electronic properties of the molecule. This research computationally investigates the effect of binding site and terminal group on the binding energy, electronic structure, and ground state geometry of the junction molecule. The electrode tips are modeled from the Face-Centered Cubic (FCC) (111) face of a gold crystal, and the molecules of interest consist of a benzene ring with either thiol or amine terminal groups. Future studies will include the application of a voltage bias to measure the conductance of the systems, and investigation into how the dynamics of the junction affect that conductance.
Abstract: Molecular junctions are the smallest form of nanoelectronic circuits, consisting of one molecule bound between two electrodes. The properties of these junctions have been of great interest to the scientific community for decades; however, there is still much unknown about the transport of electrons through the junction, and how it is affected by various physical and electronic properties of the molecule. This research computationally investigates the effect of binding site and terminal group on the binding energy, electronic structure, and ground state geometry of the junction molecule. The electrode tips are modeled from the Face-Centered Cubic (FCC) (111) face of a gold crystal, and the molecules of interest consist of a benzene ring with either thiol or amine terminal groups. Future studies will include the application of a voltage bias to measure the conductance of the systems, and investigation into how the dynamics of the junction affect that conductance.
Genome Science & Technology
Sarah Cooper
Graduate Student, Genome Science & Technology
Title: Identifying Accurate Approaches for Modeling Aquacob(II)alamin with Density Functional Theory
Abstract: Cobalamins, such as vitamin B12, act as cofactors employed by enzymes like isomerases and methyltransferases, giving them a vital role in energy production and metabolism. These molecules feature a cobalt atom bound to a corrin ring decorated with various amide groups and a 5,6-dimethylbenzimidazole (DMB) group that can covalently interact, occupying the lower axial position. The Co(III) state exists as a hexacoordinate structure comprised of the equatorial tetracoordinate corrin ring and two axial groups, while in the crystal structure the Co(II) state exists as a pentacoordinate structure. Previous work in modeling the Co(II) state has been unable to show this pentacoordinate geometry. Here we use density functional theory to model Co(II) states of aquacobalamin using N-methylbenzimidazole to represent the DMB group. Several different parameters were tested in an attempt to form the pentacoordinate structure by introduction of explicit water molecules and explicit solvent, use of different basis sets, and the addition of dispersion corrections. The interaction energies and bond distances of the axial ligands were calculated to determine whether or not a pentacoordinate structure was achieved. The results show that while it was initially suspected that introduction of parameters such as dispersion corrections, implicit and explicit solvent, and increasing the basis set used for the calculations would best model this system, this was not necessarily the case. Exclusion of dispersion corrections, use of implicit solvent with a larger basis set, and no explicit water molecules yielded the best agreement between thermal energies and ligand distances based on the data collected. Although aquacob(II)alamin is formally pentacoordinate in crystal structures, we find that in biotic systems, water molecules loosely associate with and partially fill the vacant site. The variability in the Co(II) ligand bond lengths underscores the necessity to thoroughly benchmark computational methods for predicting enzymatic mechanisms.
Abstract: Cobalamins, such as vitamin B12, act as cofactors employed by enzymes like isomerases and methyltransferases, giving them a vital role in energy production and metabolism. These molecules feature a cobalt atom bound to a corrin ring decorated with various amide groups and a 5,6-dimethylbenzimidazole (DMB) group that can covalently interact, occupying the lower axial position. The Co(III) state exists as a hexacoordinate structure comprised of the equatorial tetracoordinate corrin ring and two axial groups, while in the crystal structure the Co(II) state exists as a pentacoordinate structure. Previous work in modeling the Co(II) state has been unable to show this pentacoordinate geometry. Here we use density functional theory to model Co(II) states of aquacobalamin using N-methylbenzimidazole to represent the DMB group. Several different parameters were tested in an attempt to form the pentacoordinate structure by introduction of explicit water molecules and explicit solvent, use of different basis sets, and the addition of dispersion corrections. The interaction energies and bond distances of the axial ligands were calculated to determine whether or not a pentacoordinate structure was achieved. The results show that while it was initially suspected that introduction of parameters such as dispersion corrections, implicit and explicit solvent, and increasing the basis set used for the calculations would best model this system, this was not necessarily the case. Exclusion of dispersion corrections, use of implicit solvent with a larger basis set, and no explicit water molecules yielded the best agreement between thermal energies and ligand distances based on the data collected. Although aquacob(II)alamin is formally pentacoordinate in crystal structures, we find that in biotic systems, water molecules loosely associate with and partially fill the vacant site. The variability in the Co(II) ligand bond lengths underscores the necessity to thoroughly benchmark computational methods for predicting enzymatic mechanisms.